The most common and most likely answer to this crossword clue is the 9 letter word TRANSEPTS
I've seen this crossword clue in The Guardian
T
R
A
N
S
E
P
T
S
More clues leading to the result TRANSEPTS
Buddy explains!
The straight part
We know that "arms in sacred place" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case arms in sacred place = transepts.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.
What does TRANSEPTS mean?
TRANSEPTS noun- The transversal part of a church, which crosses at right angles to the greatest length, and between the nave and choir. In the basilicas, this had often no projection at its two ends. In Gothic churches these project greatly, and should be called the arms of the transept. It is common, however, to speak of the arms themselves as the transepts.